Conformational Changes below the Tm: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A
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- 作者：Eric D. Merkley ; Brady Bernard ; Valerie Daggett
- 刊名：Biochemistry
- 出版年：2008
- 出版时间：January 22, 2008
- 年：2008
- 卷：47
- 期：3
- 页码：880 - 892
- 全文大小：987K
- 年卷期：v.47,no.3(January 22, 2008)
- ISSN：1520-4995
文摘
Recent work suggests that some native conformations of proteins can vary with temperature.To obtain an atomic-level description of this structural and conformational variation, we have performedall-atom, explicit-solvent molecular dynamics simulations of bovine pancreatic ribonuclease A (RNaseA) up to its melting temperature (Tm 
337 K). RNase A has a thermal pretransition near 320 K [Stelea,S. D., Pancoska, P., Benight, A. S., and Keiderling, T. A. (2001) Protein Sci. 10, 970-978]. Our simulationsidentify a conformational change that coincides with this pretransition. Between 310 and 320 K, there isa small but significant decrease in the number of native contacts, 
-sheet hydrogen bonding, and deviationof backbone conformation from the starting structure, and an increase in the number of nonnative contacts.Native contacts are lost in -sheet regions and in 
1, partially due to movement of 1 away from the-sheet core. At 330 and 340 K, a nonnative helical segment of residues 15-20 forms, corresponding toa helix observed in the N-terminal domain-swapped dimer [Liu, Y. S., Hart, P. J., Schulnegger, M. P.,and Eisenberg, D. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 3437-3432]. The conformations observed atthe higher temperatures possess nativelike topology and overall conformation, with many native contacts,but they have a disrupted active site. We propose that these conformations may represent the native stateat elevated temperature, or the N' state. These simulations show that subtle, functionally important changesin protein conformation can occur below the Tm.
337 K). RNase A has a thermal pretransition near 320 K [Stelea,S. D., Pancoska, P., Benight, A. S., and Keiderling, T. A. (2001) Protein Sci. 10, 970-978]. Our simulationsidentify a conformational change that coincides with this pretransition. Between 310 and 320 K, there isa small but significant decrease in the number of native contacts, -sheet hydrogen bonding, and deviationof backbone conformation from the starting structure, and an increase in the number of nonnative contacts.Native contacts are lost in -sheet regions and in 1, partially due to movement of 1 away from the-sheet core. At 330 and 340 K, a nonnative helical segment of residues 15-20 forms, corresponding toa helix observed in the N-terminal domain-swapped dimer [Liu, Y. S., Hart, P. J., Schulnegger, M. P.,and Eisenberg, D. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 3437-3432]. The conformations observed atthe higher temperatures possess nativelike topology and overall conformation, with many native contacts,but they have a disrupted active site. We propose that these conformations may represent the native stateat elevated temperature, or the N' state. These simulations show that subtle, functionally important changesin protein conformation can occur below the Tm.